Atkinson booked Liverpool goalkeeper Simon Mignolet for tripping Stoke striker Mame Diouf with the goal unguarded in Wednesday’s fixture.
Stoke were 1-0 down at the time but lost 3-0 and Hughes argued “everybody” knew it should have been a red card.
“I don’t see why he
should be refereeing this weekend,” he added.
“My feelings reflect everybody else’s view: the referees who reviewed it since and everybody in the stadium, apart from one.
“Those are the decisions that frustrate me as a manager – and other managers.
“Why it wasn’t made I don’t know. It was a pretty straightforward decision in my view and it wasn’t made. It denied us an opportunity to have an advantage in terms of numbers. I am angry with that.”
Atkinson will take charge of Watford’s Premier League home game against Tottenham on Saturday.